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A How-To Guide for Conducting Common Fisheries-Related Analyses in R Introductory Fisheries Analyses with R provides detailed instructions on performing basic fisheries stock assessment analyses in the R environment. Accessible to practicing fisheries scientists as well as advanced undergraduate and graduate students, the book demonstrates the flexibility and power of R, offers insight into the reproducibility of script-based analyses, and shows how the use of R leads to more efficient and productive work in fisheries science. The first three chapters present a minimal introduction to the R environment that builds a foundation for the fisheries-specific analyses in the remainder of the book. These chapters help you become familiar with R for basic fisheries analyses and graphics. Subsequent chapters focus on methods to analyze age comparisons, age-length keys, size structure, weight-length relationships, condition, abundance (from capture-recapture and depletion data), mortality rates, individual growth, and the stock-recruit relationship. The fundamental statistical methods of linear regression, analysis of variance (ANOVA), and nonlinear regression are demonstrated within the contexts of these common fisheries analyses. For each analysis, the author completely explains the R functions and provides sufficient background information so that you can confidently implement each method. Web Resource The author’s website at http://derekogle.com/IFAR/ includes the data files and R code for each chapter, enabling you to reproduce the results in the book as well as create your own scripts. The site also offers supplemental code for more advanced analyses and practice exercises for every chapter.
This publication gives an updated review of the quantity of discards in the world's marine fisheries, using information from a broad range of fisheries in all continents. A number of policy issues are discussed including a 'no discards' approach to fisheries management, the need for balance between bycatch reduction and bycatch utilisation initiatives, and concerns arising from incidental catches of marine mammals, birds and reptiles. The report also highlights the need for more robust methods of estimating discards, and the development of bycatch management plans.
Using R for Modelling and Quantitative Methods in Fisheries has evolved and been adapted from an earlier book by the same author and provides a detailed introduction to analytical methods commonly used by fishery scientists, ecologists, and advanced students using the open-source software R as a programming tool. Some knowledge of R is assumed, as this is a book about using R, but an introduction to the development and working of functions, and how one can explore the contents of R functions and packages, is provided. The example analyses proceed step-by-step using code listed in the book and from the book’s companion R package, MQMF, available from GitHub and the standard archive, CRAN. The examples are designed to be simple to modify so the reader can quickly adapt the methods described to use with their own data. A primary aim of the book is to be a useful resource to natural resource practitioners and students. Featured Chapters: Model Parameter Estimation provides a detailed explanation of the requirements and steps involved in fitting models to data, using R and, mainly, maximum likelihood methods. On Uncertainty uses R to implement bootstrapping, likelihood profiles, asymptotic errors, and Bayesian posteriors to characterize any uncertainty in an analysis. The use of the Monte Carlo Markov Chain methodology is examined in some detail. Surplus Production Models applies all the methods examined in the earlier parts of the book to conducting a stock assessment. This included fitting alternative models to the available data, characterizing the uncertainty in different ways, and projecting the optimum models forward in time as the basis for providing useful management advice.
This volume constitutes the most recent and most comprehensive consideration of the largest family of bony fishes, the Cichlidae. This book offers an integrated perspective of cichlid fishes ranging from conservation of threatened species to management of cichlids as invasive species themselves. Long-standing models of taxonomy and systematics are subjected to the most recent applications and interpretations of molecular evidence and multivariate analyses; and cichlid adaptive radiations at different scales are elucidated. The incredible diversity of endemic cichlid species in African lakes is revisited as possible examples of sympatric speciation and as serious cases for management in complex anthropogenic environments. Extreme hydrology and bathymetry as driver of micro-allopatric speciation is explored in the African riverine hotspot of diversity of the lower Congo River. Dramatic new molecular evidence draws attention to the complex taxonomy and systematics of Neotropical cichlids including the crater lakes of Central America. Molecular genetics, genomics, imaging tools and field study techniques assess the roles of natural, sexual and kin selection in shaping cichlid traits and beyond. The complex behavioral adaptations of cichlids are considered from a number of sub-disciplines including sensory biology, neurobiology, development, and evolutionary ecology. Most importantly, this volume puts forth a wealth of new interpretations, explanatory hypotheses and proposals for practical management and applications that will shape the future for these remarkable fishes in nature as well as their use as models for the study of biology.
Walleye, one of the most sought-after species of freshwater sport fishes in North America, has demonstrated appreciable declines in their numbers from their original populations since the beginning of the 20th century. Similarly, Yellow Perch, once the most commonly caught sport fish and an important commercial species in North America, have also shown declines. Compiling up-to-date information on the biology and management of Walleye, Sauger, and Yellow Perch, including research on systematics, genetics, physiology, ecology, movement, population dynamics, culture, recent case histories, and management practices, will be of interest to managers, researchers, and students who deal with these important species, particularly in light of habitat alterations, population shifts, and other biotic and abiotic factors related to a changing climate.
This book explores how we can solve the urgent problem of optimizing the use of variable, uncertain but finite fisheries resources while maintaining sustainability from a marine-ecosystem conservation perspective. It offers readers a broad understanding of the current methods and theory for sustainable exploitation of fisheries resources, and introduces recent findings and technological developments. The book is divided into three parts: Part I discusses fish stock dynamics, and illustrates how ecological processes affecting life cycles and biological interactions in marine environments lead to fish stock variability in space and time in major fish groups; small pelagic fish, demersal fish and large predatory fish. These insights shed light on the mechanisms underlying the variability in fish stocks and form the essential biological basis for fisheries management. Part II addresses the technologies and systems that monitor changes in fisheries resources and marine ecosystems using two approaches: fishery-dependent and fishery-independent data. It also describes acoustic surveys and biological sampling, as well as stock assessment methods. Part III examines management models for effectively assessing the natural variability in fisheries resources. The authors explore ways of determining the allowable catch in response to changes in stock abundance and how to incorporate ecological processes and monitoring procedures into management models. This book offers readers a broad understanding of sustainable exploitation as well as insights into fisheries management for the next generation.
The 2020 edition of The State of World Fisheries and Aquaculture has a particular focus on sustainability. This reflects a number of specific considerations. First, 2020 marks the twenty-fifth anniversary of the Code of Conduct for Responsible Fisheries (the Code). Second, several Sustainable Development Goal indicators mature in 2020. Third, FAO hosted the International Symposium on Fisheries Sustainability in late 2019, and fourth, 2020 sees the finalization of specific FAO guidelines on sustainable aquaculture growth, and on social sustainability along value chains. While Part 1 retains the format of previous editions, the structure of the rest of the publication has been revised. Part 2 opens with a special section marking the twenty fifth anniversary of the Code. It also focuses on issues coming to the fore, in particular, those related to Sustainable Development Goal 14 and its indicators for which FAO is the “custodian” agency. In addition, Part 2 covers various aspects of fisheries and aquaculture sustainability. The topics discussed range widely, from data and information systems to ocean pollution, product legality, user rights and climate change adaptation. Part 3 now forms the final part of the publication, covering projections and emerging issues such as new technologies and aquaculture biosecurity. It concludes by outlining steps towards a new vision for capture fisheries. The State of World Fisheries and Aquaculture aims to provide objective, reliable and up-to-date information to a wide audience – policymakers, managers, scientists, stakeholders and indeed everyone interested in the fisheries and aquaculture sector.